Starting phenix.real_space_refine on Thu May 15 13:15:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ut6_42531/05_2025/8ut6_42531.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ut6_42531/05_2025/8ut6_42531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ut6_42531/05_2025/8ut6_42531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ut6_42531/05_2025/8ut6_42531.map" model { file = "/net/cci-nas-00/data/ceres_data/8ut6_42531/05_2025/8ut6_42531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ut6_42531/05_2025/8ut6_42531.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 8094 2.51 5 N 2314 2.21 5 O 2584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13046 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 630 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'TRANS': 125} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 126 Planarities with less than four sites: {'UNK:plan-1': 126} Unresolved non-hydrogen planarities: 126 Chain: "H" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 535 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'TRANS': 106} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 107 Planarities with less than four sites: {'UNK:plan-1': 107} Unresolved non-hydrogen planarities: 107 Chain: "A" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3851 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 467} Chain breaks: 1 Chain: "C" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3851 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 467} Chain breaks: 1 Chain: "E" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3843 Classifications: {'peptide': 486} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 466} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 9.16, per 1000 atoms: 0.70 Number of scatterers: 13046 At special positions: 0 Unit cell: (84.1, 122.525, 145.725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2584 8.00 N 2314 7.00 C 8094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.04 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.02 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.04 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS E 466 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.04 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.04 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 473 " - pdb=" SG CYS E 477 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 601 " - " ASN A 38 " " NAG A 602 " - " ASN A 63 " " NAG A 603 " - " ASN A 133 " " NAG A 604 " - " ASN A 246 " " NAG A 605 " - " ASN A 285 " " NAG A 606 " - " ASN A 483 " " NAG B 1 " - " ASN A 165 " " NAG C 601 " - " ASN C 38 " " NAG C 602 " - " ASN C 63 " " NAG C 603 " - " ASN C 133 " " NAG C 604 " - " ASN C 246 " " NAG C 605 " - " ASN C 285 " " NAG C 606 " - " ASN C 483 " " NAG D 1 " - " ASN C 165 " " NAG E 601 " - " ASN E 38 " " NAG E 602 " - " ASN E 63 " " NAG E 603 " - " ASN E 133 " " NAG E 604 " - " ASN E 246 " " NAG E 605 " - " ASN E 285 " " NAG E 606 " - " ASN E 483 " " NAG F 1 " - " ASN E 165 " Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.4 seconds 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3176 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 43 sheets defined 28.4% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 87 through 90 Processing helix chain 'G' and resid 108 through 113 removed outlier: 3.700A pdb=" N UNK G 113 " --> pdb=" O UNK G 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 32 No H-bonds generated for 'chain 'H' and resid 30 through 32' Processing helix chain 'H' and resid 80 through 84 removed outlier: 3.783A pdb=" N UNK H 84 " --> pdb=" O UNK H 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 4.086A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLY A 78 " --> pdb=" O GLN A 75 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 196 removed outlier: 3.568A pdb=" N GLN A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 404 through 456 Processing helix chain 'A' and resid 476 through 484 Processing helix chain 'A' and resid 491 through 500 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 4.918A pdb=" N GLY C 78 " --> pdb=" O GLN C 75 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 367 through 385 Processing helix chain 'C' and resid 404 through 456 Processing helix chain 'C' and resid 474 through 483 Processing helix chain 'C' and resid 491 through 500 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 80 removed outlier: 3.710A pdb=" N ASP E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLY E 78 " --> pdb=" O GLN E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 116 Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'E' and resid 366 through 385 Processing helix chain 'E' and resid 404 through 456 Processing helix chain 'E' and resid 474 through 483 Processing helix chain 'E' and resid 491 through 500 Processing sheet with id=AA1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AA3, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.545A pdb=" N UNK G 36 " --> pdb=" O UNK G 48 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N UNK G 50 " --> pdb=" O UNK G 34 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N UNK G 34 " --> pdb=" O UNK G 50 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N UNK G 52 " --> pdb=" O UNK G 32 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N UNK G 32 " --> pdb=" O UNK G 52 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N UNK G 33 " --> pdb=" O UNK G 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.712A pdb=" N UNK H 11 " --> pdb=" O UNK H 107 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.712A pdb=" N UNK H 11 " --> pdb=" O UNK H 107 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 366 removed outlier: 4.584A pdb=" N TYR A 351 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA9, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AB1, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AB2, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.103A pdb=" N ILE A 51 " --> pdb=" O GLY A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 58 through 60 Processing sheet with id=AB4, first strand: chain 'A' and resid 100 through 101 removed outlier: 3.574A pdb=" N TYR A 257 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 100 through 101 removed outlier: 7.727A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB7, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.879A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB9, first strand: chain 'A' and resid 303 through 305 Processing sheet with id=AC1, first strand: chain 'C' and resid 360 through 366 removed outlier: 4.412A pdb=" N TYR C 351 " --> pdb=" O ASP C 366 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AC3, first strand: chain 'C' and resid 40 through 41 Processing sheet with id=AC4, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC5, first strand: chain 'C' and resid 51 through 52 removed outlier: 6.545A pdb=" N ILE C 51 " --> pdb=" O GLY C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.766A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 100 through 101 removed outlier: 5.237A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 100 through 101 removed outlier: 7.679A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AD1, first strand: chain 'C' and resid 136 through 140 removed outlier: 4.567A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD3, first strand: chain 'C' and resid 281 through 283 removed outlier: 4.237A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 303 through 305 Processing sheet with id=AD5, first strand: chain 'E' and resid 361 through 365 Processing sheet with id=AD6, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AD7, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD8, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD9, first strand: chain 'E' and resid 51 through 54 removed outlier: 6.029A pdb=" N ILE E 51 " --> pdb=" O GLY E 275 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N CYS E 277 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP E 53 " --> pdb=" O CYS E 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.729A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 100 through 101 removed outlier: 4.959A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 100 through 101 removed outlier: 7.830A pdb=" N ILE E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 136 through 140 Processing sheet with id=AE5, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AE6, first strand: chain 'E' and resid 281 through 283 removed outlier: 4.265A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 303 through 305 606 hydrogen bonds defined for protein. 1629 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.41 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4407 1.34 - 1.47: 3094 1.47 - 1.59: 5707 1.59 - 1.72: 1 1.72 - 1.84: 72 Bond restraints: 13281 Sorted by residual: bond pdb=" CG PRO C 162 " pdb=" CD PRO C 162 " ideal model delta sigma weight residual 1.503 1.379 0.124 3.40e-02 8.65e+02 1.32e+01 bond pdb=" CA UNK G 118 " pdb=" CB UNK G 118 " ideal model delta sigma weight residual 1.530 1.475 0.055 2.00e-02 2.50e+03 7.56e+00 bond pdb=" CB PRO C 162 " pdb=" CG PRO C 162 " ideal model delta sigma weight residual 1.492 1.620 -0.128 5.00e-02 4.00e+02 6.53e+00 bond pdb=" N PRO C 162 " pdb=" CD PRO C 162 " ideal model delta sigma weight residual 1.473 1.507 -0.034 1.40e-02 5.10e+03 5.96e+00 bond pdb=" CA UNK H 65 " pdb=" CB UNK H 65 " ideal model delta sigma weight residual 1.530 1.486 0.044 2.00e-02 2.50e+03 4.75e+00 ... (remaining 13276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 17546 2.59 - 5.17: 442 5.17 - 7.76: 29 7.76 - 10.34: 8 10.34 - 12.93: 2 Bond angle restraints: 18027 Sorted by residual: angle pdb=" CA PRO C 162 " pdb=" N PRO C 162 " pdb=" CD PRO C 162 " ideal model delta sigma weight residual 112.00 99.07 12.93 1.40e+00 5.10e-01 8.52e+01 angle pdb=" N PRO C 162 " pdb=" CD PRO C 162 " pdb=" CG PRO C 162 " ideal model delta sigma weight residual 103.20 95.04 8.16 1.50e+00 4.44e-01 2.96e+01 angle pdb=" C UNK H 99 " pdb=" N UNK H 100 " pdb=" CA UNK H 100 " ideal model delta sigma weight residual 121.70 114.70 7.00 1.80e+00 3.09e-01 1.51e+01 angle pdb=" CB MET A 168 " pdb=" CG MET A 168 " pdb=" SD MET A 168 " ideal model delta sigma weight residual 112.70 102.44 10.26 3.00e+00 1.11e-01 1.17e+01 angle pdb=" N ARG C 354 " pdb=" CA ARG C 354 " pdb=" C ARG C 354 " ideal model delta sigma weight residual 109.24 103.65 5.59 1.67e+00 3.59e-01 1.12e+01 ... (remaining 18022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7655 17.99 - 35.98: 464 35.98 - 53.96: 158 53.96 - 71.95: 44 71.95 - 89.94: 15 Dihedral angle restraints: 8336 sinusoidal: 3427 harmonic: 4909 Sorted by residual: dihedral pdb=" CB CYS C 52 " pdb=" SG CYS C 52 " pdb=" SG CYS C 277 " pdb=" CB CYS C 277 " ideal model delta sinusoidal sigma weight residual 93.00 43.25 49.75 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CA LYS C 276 " pdb=" C LYS C 276 " pdb=" N CYS C 277 " pdb=" CA CYS C 277 " ideal model delta harmonic sigma weight residual -180.00 -153.69 -26.31 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CB CYS A 64 " pdb=" SG CYS A 64 " pdb=" SG CYS A 76 " pdb=" CB CYS A 76 " ideal model delta sinusoidal sigma weight residual -86.00 -126.91 40.91 1 1.00e+01 1.00e-02 2.35e+01 ... (remaining 8333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1554 0.053 - 0.105: 418 0.105 - 0.158: 98 0.158 - 0.210: 7 0.210 - 0.263: 5 Chirality restraints: 2082 Sorted by residual: chirality pdb=" C1 NAG A 606 " pdb=" ND2 ASN A 483 " pdb=" C2 NAG A 606 " pdb=" O5 NAG A 606 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA PRO C 162 " pdb=" N PRO C 162 " pdb=" C PRO C 162 " pdb=" CB PRO C 162 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1 NAG A 604 " pdb=" ND2 ASN A 246 " pdb=" C2 NAG A 604 " pdb=" O5 NAG A 604 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 2079 not shown) Planarity restraints: 2378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 161 " -0.095 5.00e-02 4.00e+02 1.32e-01 2.80e+01 pdb=" N PRO C 162 " 0.228 5.00e-02 4.00e+02 pdb=" CA PRO C 162 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO C 162 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA UNK H 99 " -0.020 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C UNK H 99 " 0.067 2.00e-02 2.50e+03 pdb=" O UNK H 99 " -0.025 2.00e-02 2.50e+03 pdb=" N UNK H 100 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK G 116 " 0.020 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C UNK G 116 " -0.067 2.00e-02 2.50e+03 pdb=" O UNK G 116 " 0.025 2.00e-02 2.50e+03 pdb=" N UNK G 117 " 0.022 2.00e-02 2.50e+03 ... (remaining 2375 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 222 2.65 - 3.21: 11261 3.21 - 3.77: 20438 3.77 - 4.34: 29146 4.34 - 4.90: 47705 Nonbonded interactions: 108772 Sorted by model distance: nonbonded pdb=" O ASP E 438 " pdb=" OG SER E 442 " model vdw 2.085 3.040 nonbonded pdb=" NE2 GLN C 210 " pdb=" OD2 ASP E 101 " model vdw 2.144 3.120 nonbonded pdb=" OD2 ASP A 408 " pdb=" OG SER E 110 " model vdw 2.171 3.040 nonbonded pdb=" NZ LYS A 380 " pdb=" OE1 GLU A 432 " model vdw 2.179 3.120 nonbonded pdb=" OD1 ASN C 121 " pdb=" NZ LYS C 259 " model vdw 2.208 3.120 ... (remaining 108767 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 501 or resid 601 through 606)) selection = (chain 'C' and (resid 8 through 501 or resid 601 through 606)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 32.030 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 13323 Z= 0.264 Angle : 0.956 12.926 18135 Z= 0.495 Chirality : 0.052 0.263 2082 Planarity : 0.006 0.132 2357 Dihedral : 13.948 89.941 5106 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 13.70 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 1448 helix: 1.40 (0.23), residues: 351 sheet: 0.56 (0.28), residues: 294 loop : -0.29 (0.19), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 421 HIS 0.009 0.001 HIS A 156 PHE 0.030 0.002 PHE A 353 TYR 0.020 0.002 TYR E 195 ARG 0.010 0.001 ARG E 109 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 21) link_NAG-ASN : angle 1.80027 ( 63) link_BETA1-4 : bond 0.00230 ( 3) link_BETA1-4 : angle 2.47823 ( 9) hydrogen bonds : bond 0.11585 ( 568) hydrogen bonds : angle 7.06587 ( 1629) SS BOND : bond 0.00369 ( 18) SS BOND : angle 2.05888 ( 36) covalent geometry : bond 0.00583 (13281) covalent geometry : angle 0.94663 (18027) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7393 (t) cc_final: 0.6975 (p) REVERT: A 415 ASP cc_start: 0.7405 (t0) cc_final: 0.6859 (m-30) REVERT: C 382 ASN cc_start: 0.7884 (t0) cc_final: 0.7603 (t0) outliers start: 0 outliers final: 1 residues processed: 133 average time/residue: 1.1757 time to fit residues: 172.2535 Evaluate side-chains 121 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 150 optimal weight: 0.0020 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 57 GLN A 75 GLN A 211 GLN A 295 GLN A 355 HIS A 454 GLN C 56 HIS C 363 GLN C 435 HIS E 363 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.166570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.147548 restraints weight = 15198.596| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.56 r_work: 0.3561 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13323 Z= 0.187 Angle : 0.618 9.717 18135 Z= 0.321 Chirality : 0.044 0.239 2082 Planarity : 0.005 0.061 2357 Dihedral : 5.626 59.865 2314 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.96 % Allowed : 12.06 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.20), residues: 1448 helix: 1.91 (0.24), residues: 353 sheet: 0.17 (0.28), residues: 273 loop : -0.35 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 421 HIS 0.005 0.001 HIS A 184 PHE 0.018 0.002 PHE A 353 TYR 0.013 0.002 TYR C 486 ARG 0.006 0.001 ARG C 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 21) link_NAG-ASN : angle 1.72288 ( 63) link_BETA1-4 : bond 0.00136 ( 3) link_BETA1-4 : angle 2.35931 ( 9) hydrogen bonds : bond 0.04580 ( 568) hydrogen bonds : angle 5.69859 ( 1629) SS BOND : bond 0.00564 ( 18) SS BOND : angle 1.28310 ( 36) covalent geometry : bond 0.00413 (13281) covalent geometry : angle 0.60683 (18027) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 1.337 Fit side-chains revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7254 (mttt) cc_final: 0.6973 (ttmm) REVERT: A 340 GLU cc_start: 0.6487 (mt-10) cc_final: 0.6127 (tt0) REVERT: A 344 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.5706 (mp0) REVERT: A 396 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7006 (mt-10) REVERT: C 382 ASN cc_start: 0.8009 (t0) cc_final: 0.7708 (t0) REVERT: E 139 CYS cc_start: 0.6848 (m) cc_final: 0.6557 (m) REVERT: E 168 MET cc_start: 0.6614 (tpp) cc_final: 0.6394 (mmm) REVERT: E 235 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7884 (m) REVERT: E 242 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7701 (mp) REVERT: E 261 ARG cc_start: 0.7016 (mmt90) cc_final: 0.6097 (ptt180) outliers start: 25 outliers final: 8 residues processed: 149 average time/residue: 1.1850 time to fit residues: 194.0261 Evaluate side-chains 129 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 242 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 72 optimal weight: 0.0570 overall best weight: 1.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 75 GLN A 211 GLN A 488 HIS C 363 GLN C 435 HIS E 96 ASN E 211 GLN E 312 ASN E 363 GLN E 454 GLN E 497 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.163356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.144493 restraints weight = 15375.151| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.55 r_work: 0.3506 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13323 Z= 0.192 Angle : 0.601 13.696 18135 Z= 0.308 Chirality : 0.044 0.230 2082 Planarity : 0.004 0.048 2357 Dihedral : 5.310 47.820 2312 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.27 % Allowed : 13.00 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.20), residues: 1448 helix: 1.88 (0.26), residues: 353 sheet: -0.27 (0.28), residues: 267 loop : -0.51 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 234 HIS 0.006 0.001 HIS A 184 PHE 0.015 0.002 PHE A 353 TYR 0.011 0.002 TYR E 195 ARG 0.005 0.000 ARG C 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 21) link_NAG-ASN : angle 1.79325 ( 63) link_BETA1-4 : bond 0.00233 ( 3) link_BETA1-4 : angle 2.37081 ( 9) hydrogen bonds : bond 0.04349 ( 568) hydrogen bonds : angle 5.57656 ( 1629) SS BOND : bond 0.00395 ( 18) SS BOND : angle 1.05954 ( 36) covalent geometry : bond 0.00426 (13281) covalent geometry : angle 0.58904 (18027) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7533 (t) cc_final: 0.7133 (p) REVERT: A 340 GLU cc_start: 0.6657 (mt-10) cc_final: 0.6276 (tt0) REVERT: A 344 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.5739 (mp0) REVERT: A 396 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: C 33 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7546 (mt0) REVERT: C 382 ASN cc_start: 0.8055 (t0) cc_final: 0.7757 (t0) REVERT: E 139 CYS cc_start: 0.6974 (m) cc_final: 0.6681 (m) REVERT: E 242 ILE cc_start: 0.8017 (mt) cc_final: 0.7772 (mp) REVERT: E 261 ARG cc_start: 0.7101 (mmt90) cc_final: 0.6154 (ptt180) outliers start: 29 outliers final: 9 residues processed: 159 average time/residue: 1.2319 time to fit residues: 214.2759 Evaluate side-chains 133 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 33 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 187 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 111 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN C 341 ASN C 363 GLN C 435 HIS E 296 ASN E 312 ASN E 363 GLN E 407 GLN E 497 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.164978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.146119 restraints weight = 15288.189| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.56 r_work: 0.3544 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13323 Z= 0.140 Angle : 0.535 11.904 18135 Z= 0.275 Chirality : 0.042 0.230 2082 Planarity : 0.004 0.041 2357 Dihedral : 4.980 44.179 2312 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.66 % Allowed : 12.84 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.20), residues: 1448 helix: 1.99 (0.26), residues: 351 sheet: -0.42 (0.28), residues: 279 loop : -0.52 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 421 HIS 0.003 0.001 HIS A 184 PHE 0.014 0.001 PHE A 353 TYR 0.010 0.001 TYR E 491 ARG 0.004 0.000 ARG E 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 21) link_NAG-ASN : angle 1.66742 ( 63) link_BETA1-4 : bond 0.00318 ( 3) link_BETA1-4 : angle 2.16737 ( 9) hydrogen bonds : bond 0.03952 ( 568) hydrogen bonds : angle 5.38641 ( 1629) SS BOND : bond 0.00407 ( 18) SS BOND : angle 1.10323 ( 36) covalent geometry : bond 0.00304 (13281) covalent geometry : angle 0.52269 (18027) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7485 (t) cc_final: 0.7127 (p) REVERT: A 82 LYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6910 (ttmm) REVERT: A 340 GLU cc_start: 0.6589 (mt-10) cc_final: 0.6162 (tt0) REVERT: A 344 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.5812 (mp0) REVERT: A 375 ASP cc_start: 0.7844 (m-30) cc_final: 0.7609 (m-30) REVERT: A 396 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7427 (pm20) REVERT: C 382 ASN cc_start: 0.8043 (t0) cc_final: 0.7711 (t0) REVERT: E 139 CYS cc_start: 0.6839 (m) cc_final: 0.6532 (m) REVERT: E 242 ILE cc_start: 0.8034 (mt) cc_final: 0.7772 (mp) REVERT: E 261 ARG cc_start: 0.7093 (mmt90) cc_final: 0.6150 (ptt180) REVERT: E 401 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6542 (pm20) outliers start: 34 outliers final: 11 residues processed: 154 average time/residue: 1.2547 time to fit residues: 210.8652 Evaluate side-chains 135 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 371 GLN Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 401 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 32 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 454 GLN ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 ASN E 197 GLN E 296 ASN E 312 ASN E 363 GLN E 407 GLN E 497 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.157696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.140481 restraints weight = 15501.602| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.49 r_work: 0.3460 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 13323 Z= 0.365 Angle : 0.779 15.337 18135 Z= 0.393 Chirality : 0.050 0.253 2082 Planarity : 0.006 0.058 2357 Dihedral : 6.433 58.451 2312 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.74 % Allowed : 13.39 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.20), residues: 1448 helix: 1.27 (0.26), residues: 353 sheet: -0.95 (0.27), residues: 273 loop : -0.94 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 234 HIS 0.009 0.002 HIS E 18 PHE 0.019 0.003 PHE C 87 TYR 0.017 0.003 TYR C 161 ARG 0.008 0.001 ARG C 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 21) link_NAG-ASN : angle 2.17758 ( 63) link_BETA1-4 : bond 0.00199 ( 3) link_BETA1-4 : angle 3.18312 ( 9) hydrogen bonds : bond 0.04945 ( 568) hydrogen bonds : angle 6.12509 ( 1629) SS BOND : bond 0.00643 ( 18) SS BOND : angle 1.32703 ( 36) covalent geometry : bond 0.00833 (13281) covalent geometry : angle 0.76545 (18027) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.7191 (ttmm) REVERT: A 189 LYS cc_start: 0.7471 (mttt) cc_final: 0.6839 (mtpm) REVERT: A 340 GLU cc_start: 0.6691 (mt-10) cc_final: 0.6337 (tt0) REVERT: A 344 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.5737 (mp0) REVERT: A 385 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7873 (mp) REVERT: C 33 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7642 (mt0) REVERT: C 382 ASN cc_start: 0.8117 (t0) cc_final: 0.7818 (t0) REVERT: E 139 CYS cc_start: 0.7060 (m) cc_final: 0.6812 (m) REVERT: E 197 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.7033 (pt0) REVERT: E 201 ARG cc_start: 0.7602 (ptt-90) cc_final: 0.7390 (ptt-90) REVERT: E 208 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7221 (ptt180) REVERT: E 242 ILE cc_start: 0.8103 (mt) cc_final: 0.7896 (mp) REVERT: E 261 ARG cc_start: 0.7274 (mmt90) cc_final: 0.6307 (ptt180) REVERT: E 299 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7927 (mtp85) outliers start: 35 outliers final: 12 residues processed: 152 average time/residue: 1.3942 time to fit residues: 229.9351 Evaluate side-chains 132 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 33 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 299 ARG Chi-restraints excluded: chain E residue 335 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 160 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 16 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 153 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 454 GLN A 497 ASN C 18 HIS C 341 ASN ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 GLN E 497 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.162318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.145354 restraints weight = 15470.741| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.46 r_work: 0.3514 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13323 Z= 0.152 Angle : 0.572 12.780 18135 Z= 0.291 Chirality : 0.042 0.234 2082 Planarity : 0.004 0.047 2357 Dihedral : 5.514 46.037 2312 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.43 % Allowed : 14.33 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.20), residues: 1448 helix: 1.74 (0.26), residues: 353 sheet: -0.93 (0.27), residues: 274 loop : -0.90 (0.19), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 421 HIS 0.007 0.001 HIS A 17 PHE 0.013 0.001 PHE A 353 TYR 0.011 0.002 TYR C 94 ARG 0.003 0.000 ARG C 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 21) link_NAG-ASN : angle 1.86901 ( 63) link_BETA1-4 : bond 0.00192 ( 3) link_BETA1-4 : angle 2.17637 ( 9) hydrogen bonds : bond 0.04044 ( 568) hydrogen bonds : angle 5.64648 ( 1629) SS BOND : bond 0.00376 ( 18) SS BOND : angle 0.96846 ( 36) covalent geometry : bond 0.00335 (13281) covalent geometry : angle 0.55949 (18027) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7439 (t) cc_final: 0.7079 (p) REVERT: A 82 LYS cc_start: 0.7324 (OUTLIER) cc_final: 0.7088 (ttmm) REVERT: A 312 ASN cc_start: 0.7810 (t0) cc_final: 0.7492 (p0) REVERT: A 340 GLU cc_start: 0.6569 (mt-10) cc_final: 0.6185 (tt0) REVERT: A 344 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.5748 (mp0) REVERT: A 385 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7816 (mp) REVERT: A 396 GLU cc_start: 0.7578 (mp0) cc_final: 0.7274 (pm20) REVERT: C 382 ASN cc_start: 0.8012 (t0) cc_final: 0.7721 (t0) REVERT: E 139 CYS cc_start: 0.6827 (m) cc_final: 0.6555 (m) REVERT: E 242 ILE cc_start: 0.8039 (mt) cc_final: 0.7787 (mp) REVERT: E 261 ARG cc_start: 0.7143 (mmt90) cc_final: 0.6173 (ptt180) outliers start: 31 outliers final: 12 residues processed: 151 average time/residue: 1.2949 time to fit residues: 213.2100 Evaluate side-chains 135 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 335 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 15 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 363 GLN A 454 GLN C 18 HIS C 341 ASN C 363 GLN E 197 GLN E 363 GLN E 497 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.158540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.139113 restraints weight = 15598.161| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.65 r_work: 0.3474 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 13323 Z= 0.313 Angle : 0.707 14.664 18135 Z= 0.355 Chirality : 0.048 0.243 2082 Planarity : 0.005 0.054 2357 Dihedral : 6.161 52.649 2312 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.58 % Allowed : 14.64 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.20), residues: 1448 helix: 1.40 (0.26), residues: 355 sheet: -1.14 (0.26), residues: 273 loop : -1.01 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.013 0.002 HIS C 18 PHE 0.015 0.002 PHE C 87 TYR 0.014 0.002 TYR C 161 ARG 0.007 0.001 ARG C 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 21) link_NAG-ASN : angle 2.11529 ( 63) link_BETA1-4 : bond 0.00130 ( 3) link_BETA1-4 : angle 2.84021 ( 9) hydrogen bonds : bond 0.04587 ( 568) hydrogen bonds : angle 5.93505 ( 1629) SS BOND : bond 0.00539 ( 18) SS BOND : angle 1.10168 ( 36) covalent geometry : bond 0.00717 (13281) covalent geometry : angle 0.69367 (18027) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.7043 (ttmm) REVERT: A 172 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.6859 (mp0) REVERT: A 189 LYS cc_start: 0.7400 (mttt) cc_final: 0.6707 (mtpm) REVERT: A 312 ASN cc_start: 0.7801 (t0) cc_final: 0.7470 (p0) REVERT: A 340 GLU cc_start: 0.6651 (mt-10) cc_final: 0.6272 (tt0) REVERT: A 344 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.5841 (mp0) REVERT: A 385 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7739 (mp) REVERT: A 396 GLU cc_start: 0.7753 (mp0) cc_final: 0.7314 (pm20) REVERT: C 382 ASN cc_start: 0.8075 (t0) cc_final: 0.7790 (t0) REVERT: C 462 MET cc_start: 0.7585 (mtp) cc_final: 0.7361 (mtm) REVERT: E 139 CYS cc_start: 0.7071 (m) cc_final: 0.6823 (m) REVERT: E 197 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.6985 (pm20) REVERT: E 242 ILE cc_start: 0.8079 (mt) cc_final: 0.7823 (mp) REVERT: E 261 ARG cc_start: 0.7304 (mmt90) cc_final: 0.6115 (ptt180) outliers start: 33 outliers final: 15 residues processed: 145 average time/residue: 1.2405 time to fit residues: 197.2647 Evaluate side-chains 133 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain E residue 335 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 19 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 454 GLN C 18 HIS C 341 ASN E 197 GLN E 363 GLN E 497 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.160927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.141644 restraints weight = 15587.700| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.65 r_work: 0.3500 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13323 Z= 0.193 Angle : 0.607 13.218 18135 Z= 0.307 Chirality : 0.043 0.237 2082 Planarity : 0.004 0.051 2357 Dihedral : 5.825 55.223 2312 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.19 % Allowed : 15.11 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.20), residues: 1448 helix: 1.59 (0.26), residues: 355 sheet: -1.09 (0.26), residues: 280 loop : -0.98 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 127 HIS 0.004 0.001 HIS A 17 PHE 0.011 0.002 PHE E 125 TYR 0.017 0.002 TYR E 195 ARG 0.005 0.000 ARG A 261 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 21) link_NAG-ASN : angle 1.97131 ( 63) link_BETA1-4 : bond 0.00131 ( 3) link_BETA1-4 : angle 2.30997 ( 9) hydrogen bonds : bond 0.04166 ( 568) hydrogen bonds : angle 5.70750 ( 1629) SS BOND : bond 0.00404 ( 18) SS BOND : angle 0.95374 ( 36) covalent geometry : bond 0.00433 (13281) covalent geometry : angle 0.59403 (18027) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 1.306 Fit side-chains revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.7020 (ttmm) REVERT: A 189 LYS cc_start: 0.7318 (mttt) cc_final: 0.6622 (mtpm) REVERT: A 312 ASN cc_start: 0.7733 (t0) cc_final: 0.7442 (p0) REVERT: A 340 GLU cc_start: 0.6539 (mt-10) cc_final: 0.6212 (tt0) REVERT: A 385 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7650 (mp) REVERT: A 396 GLU cc_start: 0.7654 (mp0) cc_final: 0.7276 (pm20) REVERT: C 33 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7627 (mt0) REVERT: C 344 GLU cc_start: 0.7228 (mt-10) cc_final: 0.7011 (mt-10) REVERT: C 382 ASN cc_start: 0.8043 (t0) cc_final: 0.7757 (t0) REVERT: E 139 CYS cc_start: 0.7019 (m) cc_final: 0.6747 (m) REVERT: E 197 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7214 (pm20) REVERT: E 242 ILE cc_start: 0.8073 (mt) cc_final: 0.7804 (mp) REVERT: E 261 ARG cc_start: 0.7254 (mmt90) cc_final: 0.6060 (ptt180) outliers start: 28 outliers final: 12 residues processed: 146 average time/residue: 1.1973 time to fit residues: 191.4978 Evaluate side-chains 135 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 33 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain E residue 335 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 132 optimal weight: 0.0030 chunk 116 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 128 optimal weight: 0.0060 chunk 159 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 152 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.1810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN C 18 HIS C 341 ASN C 363 GLN E 197 GLN E 363 GLN E 497 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.161535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.141715 restraints weight = 15428.780| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.73 r_work: 0.3479 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13323 Z= 0.183 Angle : 0.593 12.931 18135 Z= 0.300 Chirality : 0.043 0.235 2082 Planarity : 0.004 0.050 2357 Dihedral : 5.732 58.078 2312 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.72 % Allowed : 15.74 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.20), residues: 1448 helix: 1.70 (0.26), residues: 355 sheet: -1.05 (0.26), residues: 280 loop : -0.97 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 421 HIS 0.004 0.001 HIS A 18 PHE 0.011 0.002 PHE E 125 TYR 0.011 0.002 TYR E 195 ARG 0.005 0.000 ARG A 261 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 21) link_NAG-ASN : angle 1.91132 ( 63) link_BETA1-4 : bond 0.00173 ( 3) link_BETA1-4 : angle 2.24855 ( 9) hydrogen bonds : bond 0.04109 ( 568) hydrogen bonds : angle 5.61782 ( 1629) SS BOND : bond 0.00393 ( 18) SS BOND : angle 0.92984 ( 36) covalent geometry : bond 0.00411 (13281) covalent geometry : angle 0.58067 (18027) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7284 (OUTLIER) cc_final: 0.7013 (ttmm) REVERT: A 312 ASN cc_start: 0.7749 (t0) cc_final: 0.7446 (p0) REVERT: A 340 GLU cc_start: 0.6480 (mt-10) cc_final: 0.6241 (tt0) REVERT: A 385 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7706 (mp) REVERT: A 396 GLU cc_start: 0.7650 (mp0) cc_final: 0.7380 (pm20) REVERT: C 344 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6972 (mt-10) REVERT: C 382 ASN cc_start: 0.8035 (t0) cc_final: 0.7735 (t0) REVERT: E 139 CYS cc_start: 0.7060 (m) cc_final: 0.6789 (m) REVERT: E 197 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7071 (pm20) REVERT: E 242 ILE cc_start: 0.8072 (mt) cc_final: 0.7808 (mp) REVERT: E 261 ARG cc_start: 0.7222 (mmt90) cc_final: 0.6071 (ptt180) outliers start: 22 outliers final: 14 residues processed: 137 average time/residue: 1.1805 time to fit residues: 177.6896 Evaluate side-chains 135 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain E residue 335 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 135 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 75 GLN A 371 GLN A 497 ASN C 18 HIS C 341 ASN E 197 GLN E 363 GLN ** E 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.163140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.143264 restraints weight = 15508.380| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.75 r_work: 0.3501 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13323 Z= 0.147 Angle : 0.568 12.338 18135 Z= 0.287 Chirality : 0.043 0.290 2082 Planarity : 0.004 0.048 2357 Dihedral : 5.545 59.714 2312 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.80 % Allowed : 16.05 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1448 helix: 1.85 (0.26), residues: 355 sheet: -1.01 (0.26), residues: 280 loop : -0.91 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 421 HIS 0.005 0.001 HIS A 18 PHE 0.011 0.001 PHE E 353 TYR 0.013 0.001 TYR E 195 ARG 0.012 0.000 ARG A 261 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 21) link_NAG-ASN : angle 1.96288 ( 63) link_BETA1-4 : bond 0.00194 ( 3) link_BETA1-4 : angle 2.03857 ( 9) hydrogen bonds : bond 0.03956 ( 568) hydrogen bonds : angle 5.48191 ( 1629) SS BOND : bond 0.00345 ( 18) SS BOND : angle 0.87574 ( 36) covalent geometry : bond 0.00326 (13281) covalent geometry : angle 0.55401 (18027) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7498 (t) cc_final: 0.7140 (p) REVERT: A 82 LYS cc_start: 0.7246 (OUTLIER) cc_final: 0.6995 (ttmm) REVERT: A 189 LYS cc_start: 0.7309 (mttt) cc_final: 0.6650 (mtpm) REVERT: A 312 ASN cc_start: 0.7739 (t0) cc_final: 0.7438 (p0) REVERT: A 340 GLU cc_start: 0.6516 (mt-10) cc_final: 0.6264 (tt0) REVERT: A 344 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.5819 (mp0) REVERT: A 396 GLU cc_start: 0.7580 (mp0) cc_final: 0.7335 (pm20) REVERT: C 344 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6974 (mt-10) REVERT: C 382 ASN cc_start: 0.8014 (t0) cc_final: 0.7718 (t0) REVERT: E 139 CYS cc_start: 0.7032 (m) cc_final: 0.6753 (m) REVERT: E 197 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7044 (pm20) REVERT: E 242 ILE cc_start: 0.8064 (mt) cc_final: 0.7800 (mp) outliers start: 23 outliers final: 14 residues processed: 140 average time/residue: 1.3019 time to fit residues: 199.4063 Evaluate side-chains 138 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain E residue 335 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 146 optimal weight: 0.0070 chunk 10 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 54 optimal weight: 0.0000 chunk 35 optimal weight: 0.0870 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN C 18 HIS C 341 ASN C 363 GLN C 435 HIS E 363 GLN E 497 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.162161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.142231 restraints weight = 15509.951| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.74 r_work: 0.3500 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13323 Z= 0.182 Angle : 0.604 12.664 18135 Z= 0.302 Chirality : 0.044 0.364 2082 Planarity : 0.004 0.046 2357 Dihedral : 5.598 56.173 2312 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.64 % Allowed : 16.68 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.20), residues: 1448 helix: 1.81 (0.26), residues: 355 sheet: -1.02 (0.26), residues: 280 loop : -0.90 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 421 HIS 0.005 0.001 HIS A 17 PHE 0.013 0.002 PHE A 353 TYR 0.012 0.002 TYR E 195 ARG 0.011 0.001 ARG A 261 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 21) link_NAG-ASN : angle 2.26487 ( 63) link_BETA1-4 : bond 0.00136 ( 3) link_BETA1-4 : angle 2.21454 ( 9) hydrogen bonds : bond 0.04055 ( 568) hydrogen bonds : angle 5.52043 ( 1629) SS BOND : bond 0.00382 ( 18) SS BOND : angle 0.88199 ( 36) covalent geometry : bond 0.00411 (13281) covalent geometry : angle 0.58704 (18027) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8427.42 seconds wall clock time: 146 minutes 48.13 seconds (8808.13 seconds total)